def test_rangetree(self):
c_rangetree.create_tree( self.mytuple1 )
#we get our peptide out again with a large window
res = c_rangetree.query_tree( self.q1 - 1, self.ssrcalc -1,
self.q1 + 1, self.ssrcalc + 1, 1, 0)
self.assertEqual( len(res), 1)
self.assertEqual( res[0][0], 101)
#same result when lower boundary equals the value
res = c_rangetree.query_tree( self.q1 , self.ssrcalc ,
self.q1 + 1, self.ssrcalc + 1, 1, 0)
self.assertEqual( len(res), 1)
self.assertEqual( res[0][0], 101)
#no result when upper boundary equals the value
res = c_rangetree.query_tree( self.q1 - 1, self.ssrcalc -1,
self.q1, self.ssrcalc, 1, 0)
self.assertEqual( len(res), 0)
]
else:
ssrcalc_low = ssrcalc - par.ssrcalc_window
ssrcalc_high = ssrcalc + par.ssrcalc_window
precursors = [
p for p in allprecursors if p[2] != pep['peptide_key']
and p[4] > ssrcalc_low and p[4] < ssrcalc_high
]
elif not use_db:
# Use the rangetree
# correct rounding errors, s.t. we get the same results as before!
# use the rangetree
ssrcalc_low = ssrcalc - par.ssrcalc_window + 0.001
ssrcalc_high = ssrcalc + par.ssrcalc_window - 0.001
precursor_ids = tuple(
c_rangetree.query_tree(q1_low, ssrcalc_low, q1_high, ssrcalc_high))
precursors = [
parentid_lookup[myid[0]] for myid in precursor_ids
#dont select myself
if parentid_lookup[myid[0]][2] != pep['peptide_key']
]
#now calculate collisions in this area of the space
colldensity = c_getnonuis.calculate_density(transitions, precursors,
q3_low, q3_high, par.q3_window,
par.ppm)
assert MAX_UIS == 1
nonuseable = len([c for c in colldensity if c > 0])
prepare.append((nonuseable, nr_transitions, p_id, 1, exp_key))
progressm.update(1)
cursor.executemany(
collisions_per_peptide = computed_collisions
# see SRMCollider::Combinatorics::get_non_uis
non_useable_combinations = c_getnonuis.get_non_uis( collisions_per_peptide, myorder)
srm_ids = [t[1] for t in transitions]
tuples_strike1 = 0
if not nr_transitions < myorder:
tuples_strike1 = collider.choose(nr_transitions, myorder ) - len(non_useable_combinations)
###############################################################
#strike 2: it has to be locally clean
if not skip_strike2:
ssrcalc_low = ssrcalc - par.ssrcalc_window + 0.001
ssrcalc_high = ssrcalc + par.ssrcalc_window - 0.001
precursor_ids = tuple(c_rangetree.query_tree( q1_low, ssrcalc_low,
q1_high, ssrcalc_high ) )
precursors = tuple([parentid_lookup[myid[0]] for myid in precursor_ids
#dont select myself
if parentid_lookup[myid[0]][2] != pep['transition_group']])
# collisions_per_peptide: dictionary, for each key the set of interfering transitions is stored
collisions_per_peptide = c_getnonuis.calculate_collisions_per_peptide_other_ion_series(
transitions, precursors, par, q3_low, q3_high, par.q3_window, par.ppm, forceChargeCheck)
local_interferences = [t[0] for t in c_getnonuis.get_non_uis( collisions_per_peptide, 1).keys()]
tuples_2strike = []
for mytuple in tuples_strike1:
contaminated = 0.0
for dirty_t in local_interferences:
if dirty_t in mytuple: contaminated += 1.0
if contaminated <= contamination_allow: tuples_2strike.append(mytuple)